PDBsum entry 2zoa

Hydrolase

PDB id: 2zoa

Contents

Protein chains

271 a.a. *

Ligands

MLI ×2

Metals

FE2 ×4

Waters ×154

* Residue conservation analysis

PDB id:

2zoa

Name:

Hydrolase

Title:

Malonate-bound structure of the glycerophosphodiesterase from enterobacter aerogenes (gpdq) collected at 1.280 angstrom

Structure:

Phosphohydrolase. Chain: a, b. Synonym: gpdq, glycerophosphodiesterase. Engineered: yes

Source:

Enterobacter aerogenes. Organism_taxid: 548. Gene: gpdq. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.160 R-free: 0.179

Authors:

D.L.Ollis,C.J.Jackson,P.D.Carr

Key ref:

C.J.Jackson et al. (2008). Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 681-685. PubMed id: 18678932

Date:

07-May-08 Release date: 07-Oct-08

Protein chains

Q6XBH1  (GPDQ_KLEAE) -  Glycerophosphodiester phosphodiesterase GpdQ from Klebsiella aerogenes

Seq: 274 a.a.

Struc: 271 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.4.46 - glycerophosphodiester phosphodiesterase.
• Reaction: a sn-glycero-3-phosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate + H⁺

sn-glycero-3-phosphodiester + H2O = alcohol + sn-glycerol 3-phosphate + H(+) (Bound ligand (Het Group name = MLI) matches with 41.67% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Acta Crystallogr Sect F Struct Biol Cryst Commun 64:681-685 (2008)

PubMed id: 18678932

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.

C.J.Jackson, K.S.Hadler, P.D.Carr, A.J.Oakley, S.Yip, G.Schenk, D.L.Ollis.

ABSTRACT

The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 A to a final R factor of 17.1%. The structure was originally solved to 2.9 A resolution using SAD phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 A resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed.